[논문]Members of Ectocarpus siliculosus F-box Family Are Subjected to Differential Selective Forces

Mahmood, Niaz; Moosa, Mahdi Muhammad; Matin, S. Abdul; Khan, Haseena

doi:10.4051/ibc.2012.4.1.0001

Members of Ectocarpus siliculosus F-box Family Are Subjected to Differential Selective Forces 원문보기

Interdisciplinary Bio Central, v.4 no.1, 2012년, pp.1.1 - 1.7

Mahmood, Niaz (Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka) , Moosa, Mahdi Muhammad (Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka) , Matin, S. Abdul (DataSoft Systems Bangladesh Limited) , Khan, Haseena (Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka)

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Background: The F-box proteins represent one of the largest families of proteins in eukaryotes. Apart from being a component of the ubiquitin (Ub)/26 S proteasome pathways, their regulatory roles in other cellular and developmental pathways have also been reported. One interesting feature of the genes encoding the proteins of this particular family is their variable selection patterns across different lineages. This resulted in the presence of lineage specific F-box proteins across different species. Findings: In this study, 48 non-redundant F-box proteins in E. siliculosus have been identified by a homology based approach and classified into three classes based on their variable C-terminal domains. A greater number of the F-box proteins have domains similar to the ones identified in other species. On the other hand, when the proteins having unknown or no C-terminal domain (as predicted by InterProScan) were analyzed, it was found that some of them have the polyglutamine repeats. To gain evolutionary insights on the genes encoding the F-box proteins, their selection patterns were analyzed and a strong positive selection was observed which indicated the adaptation potential of the members of this family. Moreover, four lineage specific F-box genes were found in E. siliculosus with no identified homolog in any other species. Conclusions: This study describes a genome wide in silico analysis of the F-box proteins in E. siliculosus which sheds light on their evolutionary patterns. The results presented in this study provide a strong foundation to select candidate sequences for future functional analysis.

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제안 방법

Then domain annotation of all the 16,256 proteins of E. siliculosus was done by the standalone version of InterProScan43, and F-box proteins were screened by searching for the domains IPR001810, PTHR14289, PTHR22844, PTHR23123, PTHR23125 and SSF81383 using an in-house perl script (Additional File : ‘protein_search.pl’).

이론/모형

siliculosus F-box proteins. Multiple alignments of the full length F-box protein sequences were done by Clustal X version 2.0⁴¹ and phylogenetic tree was generated by MEGA 4.1 using neighbor-joining method. The proteins from FBXW, FBXL and FBXO families are shown in yellow, blue and red, respectively.
Phylogenetic tree was constructed using the neighbor-joining method⁴⁵ with bootstrap multiple alignment resampling set at 10,000 using Molecular Evolutionary Genetics Analysis (MEGA) software version 4.1⁴⁶. Uniform rates among sites and pairwise deletion of gaps was assumed for the analysis.
Synonymous and non-synonymous substitution pattern was determined using the modified Nei-Gojobori⁴⁷ method with the Jukes-Cantor correction as implemented in MEGA4.1⁴⁶.
So they have different localization signals which cannot be accurately predicted by the conventional algorithms. To address this issue, heterokont specific sub-cellular localization prediction tool known as HECTAR was used during this study. Out of the 48 proteins, 46 had no Nterminal target peptide as predicted by HECTAR.

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